Incidental Mutation 'R7408:Lcmt2'
ID 574831
Institutional Source Beutler Lab
Gene Symbol Lcmt2
Ensembl Gene ENSMUSG00000074890
Gene Name leucine carboxyl methyltransferase 2
Synonyms Tyw4
MMRRC Submission 045489-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.095) question?
Stock # R7408 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 120967773-120971179 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 120969185 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 413 (S413P)
Ref Sequence ENSEMBL: ENSMUSP00000097085 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028702] [ENSMUST00000066155] [ENSMUST00000099486] [ENSMUST00000110662] [ENSMUST00000110665] [ENSMUST00000110674] [ENSMUST00000119031]
AlphaFold Q8BYR1
Predicted Effect probably benign
Transcript: ENSMUST00000028702
SMART Domains Protein: ENSMUSP00000028702
Gene: ENSMUSG00000027259

DomainStartEndE-ValueType
Pfam:A_deaminase 1 276 1.8e-37 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000066155
SMART Domains Protein: ENSMUSP00000067133
Gene: ENSMUSG00000027259

DomainStartEndE-ValueType
Pfam:A_deaminase 16 343 1.6e-36 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000099486
AA Change: S413P

PolyPhen 2 Score 0.084 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000097085
Gene: ENSMUSG00000074890
AA Change: S413P

DomainStartEndE-ValueType
PDB:3P71|T 4 94 6e-12 PDB
SCOP:d1k3ia3 137 401 2e-15 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000110662
SMART Domains Protein: ENSMUSP00000106290
Gene: ENSMUSG00000027259

DomainStartEndE-ValueType
Pfam:A_deaminase 2 200 1.1e-28 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000110665
SMART Domains Protein: ENSMUSP00000106293
Gene: ENSMUSG00000027259

DomainStartEndE-ValueType
Pfam:A_deaminase 2 236 4.3e-24 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000110674
AA Change: S633P

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000106302
Gene: ENSMUSG00000074890
AA Change: S633P

DomainStartEndE-ValueType
Pfam:LCM 12 207 5.4e-28 PFAM
Pfam:Kelch_3 492 542 2.2e-6 PFAM
low complexity region 544 563 N/A INTRINSIC
low complexity region 647 661 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000119031
SMART Domains Protein: ENSMUSP00000113052
Gene: ENSMUSG00000027259

DomainStartEndE-ValueType
Pfam:A_deaminase 16 343 3e-44 PFAM
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 100% (71/71)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this intronless gene belongs to the highly variable methyltransferase superfamily. This gene is the inferred homolog of the Saccharomyces cerevisiae carboxymethyltransferase gene PPM2 that is essential for the synthesis of the hypermodified guanosine Wybutosine (yW). [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Agfg1 T C 1: 82,860,030 (GRCm39) F299S probably damaging Het
Arhgap32 A T 9: 32,157,220 (GRCm39) E72D probably benign Het
Arid1a G T 4: 133,408,391 (GRCm39) Q1654K unknown Het
Atp6v1f A C 6: 29,470,194 (GRCm39) H96P probably damaging Het
Cast A G 13: 74,887,960 (GRCm39) V161A probably damaging Het
Ccdc186 A T 19: 56,796,610 (GRCm39) C320S probably damaging Het
Cgn T A 3: 94,670,362 (GRCm39) K1031* probably null Het
Cnot10 T C 9: 114,460,894 (GRCm39) N92S probably benign Het
Crat C T 2: 30,294,577 (GRCm39) R497Q probably benign Het
Cstf2t T C 19: 31,060,593 (GRCm39) V43A possibly damaging Het
D930020B18Rik T C 10: 121,525,739 (GRCm39) L547P probably damaging Het
Dennd1a G A 2: 37,742,184 (GRCm39) probably null Het
Dtnb T A 12: 3,694,272 (GRCm39) probably null Het
Entpd1 A G 19: 40,727,309 (GRCm39) N486D possibly damaging Het
Fes G A 7: 80,028,410 (GRCm39) R736C probably damaging Het
Galr1 T G 18: 82,411,990 (GRCm39) Y292S probably damaging Het
Gda T A 19: 21,405,988 (GRCm39) D80V probably damaging Het
Ghr A G 15: 3,377,054 (GRCm39) C56R probably benign Het
Golgb1 A G 16: 36,718,909 (GRCm39) T313A probably damaging Het
Gpaa1 A T 15: 76,217,193 (GRCm39) D236V probably damaging Het
Gsdmc A G 15: 63,676,315 (GRCm39) S43P probably benign Het
Gsdmd A G 15: 75,738,202 (GRCm39) E295G probably damaging Het
Htatip2 A G 7: 49,409,534 (GRCm39) K96R probably benign Het
Insm1 T A 2: 146,064,711 (GRCm39) F176I probably benign Het
Itih1 T C 14: 30,665,117 (GRCm39) E36G probably benign Het
Jak1 A G 4: 101,032,379 (GRCm39) V409A probably damaging Het
Knl1 A G 2: 118,901,073 (GRCm39) I925V possibly damaging Het
Lmo7 T C 14: 102,118,389 (GRCm39) S205P probably damaging Het
Lrch3 C A 16: 32,807,113 (GRCm39) S462* probably null Het
Lrrtm2 T C 18: 35,346,688 (GRCm39) I205V possibly damaging Het
Mark3 T G 12: 111,600,223 (GRCm39) N479K probably damaging Het
Mrpl19 C T 6: 81,942,793 (GRCm39) G39D possibly damaging Het
Msh4 A G 3: 153,582,382 (GRCm39) Y497H probably benign Het
Msl2 T A 9: 100,979,316 (GRCm39) D563E probably benign Het
Mta1 G A 12: 113,095,088 (GRCm39) probably null Het
Nalcn T A 14: 123,529,272 (GRCm39) Q1401L probably benign Het
Ncapg T C 5: 45,853,135 (GRCm39) L867P probably benign Het
Nkapl T C 13: 21,652,013 (GRCm39) D200G unknown Het
Nos1 A C 5: 118,005,583 (GRCm39) E101A probably damaging Het
Npat T C 9: 53,481,216 (GRCm39) S1008P probably damaging Het
Ntng1 A G 3: 109,760,398 (GRCm39) I358T probably benign Het
Or11h6 A G 14: 50,879,852 (GRCm39) E32G probably benign Het
Or13p4 C T 4: 118,546,859 (GRCm39) M263I probably damaging Het
Or2d2b A G 7: 106,705,274 (GRCm39) S265P probably benign Het
Or4b1 T A 2: 89,980,188 (GRCm39) H54L probably benign Het
Or6c88 A G 10: 129,406,493 (GRCm39) probably benign Het
Pex1 A G 5: 3,680,222 (GRCm39) D948G probably damaging Het
Pkd1l2 A T 8: 117,755,218 (GRCm39) I1660N possibly damaging Het
Pkp2 T A 16: 16,079,537 (GRCm39) Y540N possibly damaging Het
Pkp4 T C 2: 59,142,110 (GRCm39) L471P probably damaging Het
Plekhm3 A T 1: 64,977,143 (GRCm39) M109K probably benign Het
Plekhn1 T C 4: 156,318,418 (GRCm39) N68S probably benign Het
Pramel7 T A 2: 87,321,189 (GRCm39) D282V possibly damaging Het
Pxdn T C 12: 30,040,944 (GRCm39) Y407H probably benign Het
Rab3ip T C 10: 116,773,546 (GRCm39) D89G possibly damaging Het
Rad17 G A 13: 100,766,019 (GRCm39) Q370* probably null Het
Robo4 T C 9: 37,322,277 (GRCm39) C751R probably benign Het
Sez6 A G 11: 77,844,356 (GRCm39) T60A probably damaging Het
Socs4 A G 14: 47,527,296 (GRCm39) H77R probably benign Het
Srrm3 T A 5: 135,881,060 (GRCm39) M120K probably benign Het
Steap4 A T 5: 8,028,453 (GRCm39) I344F probably benign Het
Stk36 T A 1: 74,672,725 (GRCm39) F989Y probably damaging Het
Toporsl A T 4: 52,612,108 (GRCm39) Q667L probably benign Het
Tspan17 T C 13: 54,937,466 (GRCm39) F20S probably benign Het
Tubgcp3 G A 8: 12,711,359 (GRCm39) Q65* probably null Het
Ush2a A T 1: 188,465,726 (GRCm39) I2765F probably benign Het
Vwa8 A C 14: 79,219,674 (GRCm39) probably null Het
Wdfy4 A G 14: 32,800,264 (GRCm39) V1954A Het
Xrn2 T A 2: 146,884,017 (GRCm39) probably null Het
Zfp687 C T 3: 94,914,841 (GRCm39) R1220H probably damaging Het
Other mutations in Lcmt2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02142:Lcmt2 APN 2 120,969,394 (GRCm39) missense possibly damaging 0.94
R0352:Lcmt2 UTSW 2 120,969,377 (GRCm39) missense probably benign 0.06
R0519:Lcmt2 UTSW 2 120,969,825 (GRCm39) splice site probably null
R0685:Lcmt2 UTSW 2 120,969,721 (GRCm39) missense probably benign 0.14
R1437:Lcmt2 UTSW 2 120,969,377 (GRCm39) missense probably benign 0.06
R1500:Lcmt2 UTSW 2 120,970,488 (GRCm39) missense probably benign 0.00
R1569:Lcmt2 UTSW 2 120,970,309 (GRCm39) missense probably damaging 1.00
R1612:Lcmt2 UTSW 2 120,969,601 (GRCm39) missense probably damaging 1.00
R1618:Lcmt2 UTSW 2 120,969,133 (GRCm39) missense probably damaging 0.98
R1990:Lcmt2 UTSW 2 120,970,762 (GRCm39) missense probably benign 0.07
R2091:Lcmt2 UTSW 2 120,969,097 (GRCm39) missense probably damaging 1.00
R2159:Lcmt2 UTSW 2 120,969,766 (GRCm39) missense probably damaging 1.00
R3812:Lcmt2 UTSW 2 120,969,187 (GRCm39) missense probably benign 0.01
R4725:Lcmt2 UTSW 2 120,969,911 (GRCm39) missense probably benign 0.00
R4727:Lcmt2 UTSW 2 120,969,911 (GRCm39) missense probably benign 0.00
R4968:Lcmt2 UTSW 2 120,970,217 (GRCm39) missense probably benign 0.00
R5626:Lcmt2 UTSW 2 120,969,943 (GRCm39) missense probably benign
R6246:Lcmt2 UTSW 2 120,970,870 (GRCm39) missense probably damaging 1.00
R6326:Lcmt2 UTSW 2 120,969,938 (GRCm39) nonsense probably null
R6524:Lcmt2 UTSW 2 120,969,412 (GRCm39) missense possibly damaging 0.75
R6924:Lcmt2 UTSW 2 120,970,484 (GRCm39) missense probably benign
R7282:Lcmt2 UTSW 2 120,969,271 (GRCm39) missense probably damaging 1.00
R7405:Lcmt2 UTSW 2 120,969,868 (GRCm39) missense probably benign 0.07
R8062:Lcmt2 UTSW 2 120,970,753 (GRCm39) missense possibly damaging 0.89
R8472:Lcmt2 UTSW 2 120,970,729 (GRCm39) missense probably damaging 1.00
R9414:Lcmt2 UTSW 2 120,970,621 (GRCm39) missense possibly damaging 0.81
R9569:Lcmt2 UTSW 2 120,970,522 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TGGGAGTGTGGCAATACAAC -3'
(R):5'- GGGAATCAATAGATATCCAGCCC -3'

Sequencing Primer
(F):5'- GAGTGTGGCAATACAACAAATTCAC -3'
(R):5'- TAGATATCCAGCCCTCCATTACC -3'
Posted On 2019-10-07